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A biologically meaningful co-occurrence of multiple<jats:italic>cis<\/jats:italic>-elements in a gene promoter is assessed by the combined analysis of genomic and gene expression data. Greater statistical significance is associated with a set of genes that shares a common set of regulatory motifs, while simultaneously exhibiting highly correlated gene expression under given experimental conditions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>XcisClique, the system developed in this work, is a comprehensive infrastructure that associates annotated genome and gene expression data, models known<jats:italic>cis<\/jats:italic>-elements as regular expressions, identifies maximal bicliques in a bipartite gene-motif graph; and ranks bicliques based on their computed statistical significance. Significance is a function of the probability of occurrence of those motifs in a biclique (a hypergeometric distribution), and on the new sum of absolute values statistic (SAV) that uses Spearman correlations of gene expression vectors. SAV is a statistic well-suited for this purpose as described in the discussion.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>XcisClique identifies new motif and gene combinations that might indicate as yet unidentified involvement of sets of genes in biological functions and processes. It currently supports<jats:italic>Arabidopsis thaliana<\/jats:italic>and can be adapted to other organisms, assuming the existence of annotated genomic sequences, suitable gene expression data, and identified regulatory motifs. A subset of Xcis Clique functionalities, including the motif visualization component MotifSee, source code, and supplementary material are available at<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/bioinformatics.cs.vt.edu\/xcisclique\/\" ext-link-type=\"uri\">https:\/\/bioinformatics.cs.vt.edu\/xcisclique\/<\/jats:ext-link>.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-7-218","type":"journal-article","created":{"date-parts":[[2006,4,21]],"date-time":"2006-04-21T18:21:30Z","timestamp":1145643690000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["XcisClique: analysis of regulatory bicliques"],"prefix":"10.1186","volume":"7","author":[{"given":"Amrita","family":"Pati","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cecilia","family":"Vasquez-Robinet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lenwood S","family":"Heath","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruth","family":"Grene","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"TM","family":"Murali","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2006,4,21]]},"reference":[{"key":"957_CR1","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1101\/gr.7.9.861","volume":"7","author":"JW Fickett","year":"1997","unstructured":"Fickett JW, Hatzigeorgiou AG: Eukaryotic Promoter Recognition. 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